YSMR: a video tracking and analysis program for bacterial motility

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

doi:10.1186/s12859-020-3495-9

Cited by 5 publications

(15 citation statements)

References 8 publications

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“…For quantitative data of the C. difficile swimming parameters, we recorded video files and always analysed 10 s of motility parameters per detected bacteria with the aid of the recently developed bacterial tracking programme YSMR ( Schwanbeck et al, 2020 ). We used a low magnification objective (10x) for video recording in order to monitor the swimming behaviour of a large number of bacteria (100–5,000) per video.…”

Section: Methodsmentioning

confidence: 99%

“…We applied single cell tracking using the recently developed bacterial tracking programme YSMR (Schwanbeck et al, 2020) to analyse and quantify the motility characteristics of C. difficile (see Supplementary Videos 5-7). Per track we quantified the average speed, maximal displacement to body length ratio, arc-chord FIGURE 1 | Single cell motility dependency on PVP of C. difficile 630 erm.…”

Section: The Motility Phenotype Changes In the Presence Of The High Molecular Weight Polymers Pvp And Mucinmentioning

confidence: 99%

“…We report in this study on the swimming behaviour of C. difficile and its strong dependency on the viscoelastic properties of the medium across all motile clades. A comprehensive quantitative analysis of C. difficile motility parameters on the single cell level was obtained with the aid of the bacterial tracking programme YSMR ( Schwanbeck et al, 2020 ). We hypothesise that this dependency on viscoelastic properties is an adaptation to the properties of the mucin rich lower intestines, which form the habitat of C. difficile .…”

Section: Introductionmentioning

confidence: 99%

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Clostridioides difficile Single Cell Swimming Strategy: A Novel Motility Pattern Regulated by Viscoelastic Properties of the Environment

et al. 2021

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Flagellar motility is important for the pathogenesis of many intestinal pathogens, allowing bacteria to move to their preferred ecological niche. Clostridioides difficile is currently the major cause for bacterial health care-associated intestinal infections in the western world. Most clinical strains produce peritrichous flagella and are motile in soft-agar. However, little knowledge exists on the C. difficile swimming behaviour and its regulation at the level of individual cells. We report here on the swimming strategy of C. difficile at the single cell level and its dependency on environmental parameters. A comprehensive analysis of motility parameters from several thousand bacteria was achieved with the aid of a recently developed bacterial tracking programme. C. difficile motility was found to be strongly dependent on the matrix elasticity of the medium. Long run phases of all four motile C. difficile clades were only observed in the presence of high molecular weight molecules such as polyvinylpyrrolidone (PVP) and mucin, which suggests an adaptation of the motility apparatus to the mucin-rich intestinal environment. Increasing mucin or PVP concentrations lead to longer and straighter runs with increased travelled distance per run and fewer turnarounds that result in a higher net displacement of the bacteria. The observed C. difficile swimming pattern under these conditions is characterised by bidirectional, alternating back and forth run phases, interrupted by a short stop without an apparent reorientation or tumbling phase. This motility type was not described before for peritrichous bacteria and is more similar to some previously described polar monotrichous bacteria.

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Section: Methodsmentioning

confidence: 99%

Section: The Motility Phenotype Changes In the Presence Of The High Molecular Weight Polymers Pvp And Mucinmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Clostridioides difficile Single Cell Swimming Strategy: A Novel Motility Pattern Regulated by Viscoelastic Properties of the Environment

et al. 2021

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“…We recently investigated single cell motility and swimming behavior of C. difficile with the aid of a bacterial tracking program (YSMR), which generates quantitative data on motility parameter such as speed, turning points and run lengths, simultaneously from several hundred bacteria (Schwanbeck et al, 2020). We could demonstrate that every motile C. difficile clade requires specific visco-elastic properties of the medium in order to display flagellar driven swimming motility (Schwanbeck et al, 2021). A motility pattern with long run phases only occurred when the matrix elasticity was increased by high molecular weight molecules, as for example, polyvinylpyrrolidones (PVP) or mucins.…”

Section: Introductionmentioning

confidence: 99%

“…A motility pattern with long run phases only occurred when the matrix elasticity was increased by high molecular weight molecules, as for example, polyvinylpyrrolidones (PVP) or mucins. The motility behavior of C. difficile appears thus to be well adapted to the mucin-rich mucosal layer of the gastrointestinal tract (Schwanbeck et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Clostridioides difficile minimal nutrient requirements for flagellar motility

et al. 2023

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As many gastro-intestinal pathogens, the majority of Clostridioides difficile strains express flagella together with a complete chemotaxis system. The resulting swimming motility is likely contributing to the colonization success of this important pathogen. In contrast to the well investigated general energy metabolism of C. difficile, little is known about the metabolic requirements for maintaining the ion motive force across the membrane, which in turn powers the flagellar motor. We studied here systematically the effect of various amino acids and carbohydrates on the swimming velocity of C. difficile using video microscopy in conjunction with a software based quantification of the swimming speed. Removal of individual amino acids from the medium identified proline and cysteine as the most important amino acids that power swimming motility. Glycine, which is as proline one of the few amino acids that are reduced in Stickland reactions, was not critical for swimming motility. This suggests that the ion motive force that powers the flagellar motor, is critically depending on proline reduction. A maximal and stable swimming motility was achieved with only four compounds, including the amino acids proline, cysteine and isoleucine together with a single, but interchangeable carbohydrate source such as glucose, succinate, mannose, ribose, pyruvate, trehalose, or ethanolamine. We expect that the identified “minimal motility medium” will be useful in future investigations on the flagellar motility and chemotactic behavior in C. difficile, particularly for the unambiguous identification of chemoattractants.

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Motion Enhanced Multi‐Level Tracker (MEMTrack): A Deep Learning‐Based Approach to Microrobot Tracking in Dense and Low‐Contrast Environments

Sawhney,

Karmarkar,

Leaman

et al. 2024

Advanced Intelligent Systems

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Tracking microrobots is challenging due to their minute size and high speed. In biomedical applications, this challenge is exacerbated by the dense surrounding environments with feature sizes and shapes comparable to microrobots. Herein, Motion Enhanced Multi‐level Tracker (MEMTrack) is introduced for detecting and tracking microrobots in dense and low‐contrast environments. Informed by the physics of microrobot motion, synthetic motion features for deep learning‐based object detection and a modified Simple Online and Real‐time Tracking (SORT)algorithm with interpolation are used for tracking. MEMTrack is trained and tested using bacterial micromotors in collagen (tissue phantom), achieving precision and recall of 76% and 51%, respectively. Compared to the state‐of‐the‐art baseline models, MEMTrack provides a minimum of 2.6‐fold higher precision with a reasonably high recall. MEMTrack's generalizability to unseen (aqueous) media and its versatility in tracking microrobots of different shapes, sizes, and motion characteristics are shown. Finally, it is shown that MEMTrack localizes objects with a root‐mean‐square error of less than 1.84 μm and quantifies the average speed of all tested systems with no statistically significant difference from the laboriously produced manual tracking data. MEMTrack significantly advances microrobot localization and tracking in dense and low‐contrast settings and can impact fundamental and translational microrobotic research.

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YSMR: a video tracking and analysis program for bacterial motility

Cited by 5 publications

References 8 publications

Clostridioides difficile Single Cell Swimming Strategy: A Novel Motility Pattern Regulated by Viscoelastic Properties of the Environment

Clostridioides difficile Single Cell Swimming Strategy: A Novel Motility Pattern Regulated by Viscoelastic Properties of the Environment

Clostridioides difficile minimal nutrient requirements for flagellar motility

Motion Enhanced Multi‐Level Tracker (MEMTrack): A Deep Learning‐Based Approach to Microrobot Tracking in Dense and Low‐Contrast Environments

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