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Computational Analysis of Microbial Flow Cytometry Data

This document summarizes the computational analysis steps for microbial flow cytometry data. It provides an overview of the full data analysis pipeline, from measurement to data interpretation. The pipeline includes data processing beyond the commercial instrument software. While flow cytometry can generate large amounts of quantitative, multivariate, single-cell data, no full overview of the computational analysis steps existed previously. This review aims to describe each analysis step and highlight useful computational methods, in order to standardize the analysis of microbial flow cytometry data.

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17 views1 page

Computational Analysis of Microbial Flow Cytometry Data

This document summarizes the computational analysis steps for microbial flow cytometry data. It provides an overview of the full data analysis pipeline, from measurement to data interpretation. The pipeline includes data processing beyond the commercial instrument software. While flow cytometry can generate large amounts of quantitative, multivariate, single-cell data, no full overview of the computational analysis steps existed previously. This review aims to describe each analysis step and highlight useful computational methods, in order to standardize the analysis of microbial flow cytometry data.

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gorkhmazabbaszade
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 MINIREVIEW
Applied and Environmental Science PDF • 1.2 MB
January/February 2021 Volume 6 Issue 1 e00895-20
mSystems
Volume 6, Issue 1
 https://doi.org/10.1128/mSystems.00895-20
EPUB • 782.1 KB


Feb 2021

Computational Analysis of Microbial Flow Cytometry Data

Peter Rubbens a, Ruben Props b

a FlandersMarine Institute (VLIZ), Ostend, Belgium


ARTICLE b Centerfor Microbial Ecology & Technology (CMET), Faculty of Bioscience Engineering, Ghent University,
Computational Analysis of Microbial Flow Ghent, Belgium

Cytometry Data ABSTRACT Flow cytometry is an important technology for the study of microbial communities. It
grants the ability to rapidly generate phenotypic single-cell data that are both quantitative,
View article page
multivariate and of high temporal resolution. The complexity and amount of data necessitate an
Peter Rubbens, Ruben Props and Pieter C. Dorrestein objective and streamlined data processing workflow that extends beyond commercial instrument
software. No full overview of the necessary steps regarding the computational analysis of microbial
 CITE flow cytometry data currently exists. In this review, we provide an overview of the full data analysis
pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial
Copyright © 2021 Rubbens and Props.
ecology. At every step, we highlight computational methods that are potentially useful, for which we
https://doi.org/10.1128/mSystems.00895-20  provide a short nontechnical description. We place this overview in the context of a number of open
challenges to the field and offer further motivation for the use of standardized flow cytometry in
Publisher American Society for Microbiology microbial ecology research.

eISSN 2379-5077 KEYWORDS bioinformatics, cytometry, fingerprinting, data analysis, microbial ecology, single cell,
Online January 19, 2021 multivariate statistics

Published 19 January 2021


ABSTRACT Citation Rubbens P, Props R. 2021. Computational analysis of microbial flow cytometry data. mSystems 6:e00895-20.
Flow cytometry is an important technology for the study https://doi.org/10.1128/mSystems.00895-20.
of microbial communities. It grants the ability to rapidly Editor Pieter C. Dorrestein, University of California, San Diego
generate phenotypic single-cell data that are both Copyright © 2021 Rubbens and Props. This is an open-access article distributed under the terms of the Creative
Commons Attribution 4.0 International license.
quantitative, multivariate and of high temporal
resolution. The complexity and amount of data
necessitate an objective and streamlined data

F
processing work ow that extends beyond commercial low cytometry (FCM) is a single-cell technology that provides an optical description of
instrument software. No full overview of the necessary individual particles based on scatter and fluorescence information. Microbial FCM has a
steps regarding the computational analysis of microbial long history, and its first applications in the field date back to the late 1970s to investigate the
ow cytometry data currently exists. In this review, we
physiological properties of individual cultures (1, 2). The most prevalent application in
provide an overview of the full data analysis pipeline,
ranging from measurement to data interpretation,
microbiology remains the quantification of cell population densities in a wide range of
matrices, ranging from lab cultures to marine, freshwater, soil, and fecal samples (3–8). FCM
tailored toward studies in microbial ecology. At every 
step, we highlight computational methods that are has been applied to many types of microorganisms, mostly phytoplankton and bacteria, but

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