Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.

Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimm...

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Autores principales:	Gabriel Rosser, Alexander G Fletcher, David A Wilkinson, Jennifer A de Beyer, Christian A Yates, Judith P Armitage, Philip K Maini, Ruth E Baker
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/9661b364f8864725b727c688341b69cb
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spelling	oai:doaj.org-article:9661b364f8864725b727c688341b69cb2021-11-18T05:53:29ZNovel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.1553-734X1553-735810.1371/journal.pcbi.1003276https://doaj.org/article/9661b364f8864725b727c688341b69cb2013-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24204227/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. It is therefore necessary to segment observed tracks into swimming and reorientation phases to extract useful statistics. We present novel robust analysis tools to discern these two phases in tracks. Our methods comprise a simple and effective protocol for removing spurious tracks from tracking datasets, followed by analysis based on a two-state hidden Markov model, taking advantage of the availability of mutant strains that exhibit swimming-only or reorientating-only motion to generate an empirical prior distribution. Using simulated tracks with varying levels of added noise, we validate our methods and compare them with an existing heuristic method. To our knowledge this is the first example of a systematic assessment of analysis methods in this field. The new methods are substantially more robust to noise and introduce less systematic bias than the heuristic method. We apply our methods to tracks obtained from the bacterial species Rhodobacter sphaeroides and Escherichia coli. Our results demonstrate that R. sphaeroides exhibits persistence over the course of a tumbling event, which is a novel result with important implications in the study of this and similar species.Gabriel RosserAlexander G FletcherDavid A WilkinsonJennifer A de BeyerChristian A YatesJudith P ArmitagePhilip K MainiRuth E BakerPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 10, p e1003276 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Gabriel Rosser Alexander G Fletcher David A Wilkinson Jennifer A de Beyer Christian A Yates Judith P Armitage Philip K Maini Ruth E Baker Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
description	Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. It is therefore necessary to segment observed tracks into swimming and reorientation phases to extract useful statistics. We present novel robust analysis tools to discern these two phases in tracks. Our methods comprise a simple and effective protocol for removing spurious tracks from tracking datasets, followed by analysis based on a two-state hidden Markov model, taking advantage of the availability of mutant strains that exhibit swimming-only or reorientating-only motion to generate an empirical prior distribution. Using simulated tracks with varying levels of added noise, we validate our methods and compare them with an existing heuristic method. To our knowledge this is the first example of a systematic assessment of analysis methods in this field. The new methods are substantially more robust to noise and introduce less systematic bias than the heuristic method. We apply our methods to tracks obtained from the bacterial species Rhodobacter sphaeroides and Escherichia coli. Our results demonstrate that R. sphaeroides exhibits persistence over the course of a tumbling event, which is a novel result with important implications in the study of this and similar species.
format	article
author	Gabriel Rosser Alexander G Fletcher David A Wilkinson Jennifer A de Beyer Christian A Yates Judith P Armitage Philip K Maini Ruth E Baker
author_facet	Gabriel Rosser Alexander G Fletcher David A Wilkinson Jennifer A de Beyer Christian A Yates Judith P Armitage Philip K Maini Ruth E Baker
author_sort	Gabriel Rosser
title	Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
title_short	Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
title_full	Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
title_fullStr	Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
title_full_unstemmed	Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.
title_sort	novel methods for analysing bacterial tracks reveal persistence in rhodobacter sphaeroides.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/9661b364f8864725b727c688341b69cb
work_keys_str_mv	AT gabrielrosser novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides AT alexandergfletcher novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides AT davidawilkinson novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides AT jenniferadebeyer novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides AT christianayates novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides AT judithparmitage novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides AT philipkmaini novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides AT ruthebaker novelmethodsforanalysingbacterialtracksrevealpersistenceinrhodobactersphaeroides
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Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides.

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