Explanipedia

Real-time flow cytometry to assess qualitative and quantitative responses of oral pathobionts during exposure to antiseptics Open

Ioanna Chatzigiannidou, J. Heyse, Ruben Props, Peter Rubbens, Fabian Mermans , et al. · 2024

Antiseptics are widely used in oral healthcare to prevent or treat oral diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant to standard antiseptics has sharply increased over the last few years…

Machine learning in marine ecology: an overview of techniques and applications Open

Peter Rubbens, Stephanie Brodie, Tristan Cordier, Diogo Destro Barcellos, Paul Devos , et al. · 2023

Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first…

Real-Time Flow Cytometry to assess qualitative and quantitative responses of oral pathobionts during exposure to antiseptics Open

Ioanna Chatzigiannidou, J. Heyse, Ruben Props, Peter Rubbens, Wim Teughels , et al. · 2022

Antiseptics are widely used in oral healthcare to prevent or treat oral diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant to standard antiseptics has sharply increased over the last few years…

Predicting the Presence and Abundance of Bacterial Taxa in Environmental Communities through Flow Cytometric Fingerprinting Open

J. Heyse, Florian Schattenberg, Peter Rubbens, Susann Müller, Willem Waegeman , et al. · 2021

Monitoring of microbial community composition is crucial for both microbiome management research and applications. Existing technologies, such as plating and amplicon sequencing, can become laborious and expensive when high-throughput meas…

Predicting the presence and abundance of bacterial taxa in environmental communities through flow cytometric fingerprinting Open

J. Heyse, Florian Schattenberg, Peter Rubbens, Susann Müller, Willem Waegeman , et al. · 2021

Microbiome management research and applications rely on temporally-resolved measurements of community composition. Current technologies to assess community composition either make use of cultivation or sequencing of genomic material, which…

PhenoGMM: Gaussian Mixture Modeling of Cytometry Data Quantifies Changes in Microbial Community Structure Open

Peter Rubbens, Ruben Props, Frederiek‐Maarten Kerckhof, Nico Boon, Willem Waegeman · 2021

Microorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA.

Computational Analysis of Microbial Flow Cytometry Data Open

Peter Rubbens, Ruben Props · 2021

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, multivariate and of high temporal resolution.

Cytometric fingerprints of gut microbiota predict Crohn’s disease state Open

Peter Rubbens, Ruben Props, Frederiek‐Maarten Kerckhof, Nico Boon, Willem Waegeman · 2020

Variations in the gut microbiome have been associated with changes in health state such as Crohn’s disease (CD). Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is …

Discriminating Bacterial Phenotypes at the Population and Single‐Cell Level: A Comparison of Flow Cytometry and Raman Spectroscopy Fingerprinting Open

Cristina García‐Timermans, Peter Rubbens, J. Heyse, Frederiek‐Maarten Kerckhof, Ruben Props , et al. · 2019

Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical to…

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry Open

Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon , et al. · 2019

A major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In thi…

Cyt‐Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops Open

Kamila Czechowska, Joanne Lannigan, Lili Wang, Judith Arcidiacono, Thomas M. Ashhurst , et al. · 2019

Organized by the International Society for Advancement of Cytometry (ISAC), the CYTO conference is one of the most important events for everyone interested in cytometry and quantitative single cell analysis. It is an annual assembly of cyt…

Cytometric fingerprints of gut microbiota predict Crohn’s disease state Open

Peter Rubbens, Ruben Props, Frederiek‐Maarten Kerckhof, Nico Boon, Willem Waegeman · 2019

Variations in the gut microbiome have been associated with changes in health state such as Crohn’s disease. Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow …

<i>PhenoGMM</i>: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity Open

Peter Rubbens, Ruben Props, Frederiek‐Maarten Kerckhof, Nico Boon, Willem Waegeman · 2019

Microbial flow cytometry allows to rapidly characterize microbial communities. Recent research has demonstrated a moderate to strong connection between the cytometric diversity and taxonomic diversity based on 16S rRNA gene amplicon sequen…

Learning Single‐Cell Distances from Cytometry Data Open

Bac Nguyen, Peter Rubbens, Frederiek‐Maarten Kerckhof, Nico Boon, Bernard De Baets , et al. · 2019

Recent years have seen an increased interest in employing data analysis techniques for the automated identification of cell populations in the field of cytometry. These techniques highly depend on the use of a distance metric, a function t…

Coculturing Bacteria Leads to Reduced Phenotypic Heterogeneities Open

J. Heyse, Benjamin Buysschaert, Ruben Props, Peter Rubbens, André G. Skirtach , et al. · 2019

Laboratory studies have shown the impact of phenotypic heterogeneity on the survival and functionality of isogenic populations. Because phenotypic heterogeneity plays an important role in pathogenicity and virulence, antibiotic resistance,…

Measuring phenotypic heterogeneity in isogenic bacterial populations using flow cytometry and Raman spectroscopy Open

Cristina García‐Timermans, Peter Rubbens, J. Heyse, Frederiek‐Maarten Kerckhof, Ruben Props , et al. · 2019

Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical to…

Machine learning approaches for microbial flow cytometry at the single-cell and community level Open

Peter Rubbens · 2019

Discriminating bacterial phenotypes at the population and single‐cell level: a comparison of flow cytometry and Raman spectroscopy fingerprinting Open

Cristina García‐Timermans, Peter Rubbens, J. Heyse, Frederiek‐Maarten Kerckhof, Ruben Props , et al. · 2019

Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical to…

Coculturing bacteria leads to reduced phenotypic heterogeneities Open

J. Heyse, Benjamin Buysschaert, Ruben Props, Peter Rubbens, André G. Skirtach , et al. · 2018

Isogenic bacterial populations are known to exhibit phenotypic heterogeneity at the single cell level. Because of difficulties in assessing the phenotypic heterogeneity of a single taxon in a mixed community, the importance of this deeper …

Randomized lasso associates freshwater lake-system specific bacterial taxa with heterotrophic production through flow cytometry Open

Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon , et al. · 2018

High-(HNA) and low-nucleic acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. HNA cell density often correlates strongly with heterotrophic production, while LNA cell density does not. How…

Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data Open

Ruben Props, Peter Rubbens, Michael D. Besmer, Benjamin Buysschaert, Jürg A. Sigrist , et al. · 2018

Stripping flow cytometry: How many detectors do we need for bacterial identification? Open

Peter Rubbens, Ruben Props, Cristina García‐Timermans, Nico Boon, Willem Waegeman · 2017

Multicolor approaches are challenging for microbial flow cytometry; as flow cytometers are mainly developed for biomedical applications, modern instruments contain more detectors than needed. Some of these additional fluorescence detectors…

Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities Open

Peter Rubbens, Ruben Props, Nico Boon, Willem Waegeman · 2017

Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements of up to 50,000 cells per second. However, there has not yet been a thorough survey…

Detecting phenotypes with Raman spectroscopy Open

Cristina García‐Timermans, Benjamin Buysschaert, Peter Rubbens, Frederiek‐Maarten Kerckhof, André G. Skirtach , et al. · 2017

Identifying synthetic communities using flow cytometry and machine learning Open

Peter Rubbens, Cristina García‐Timermans, Ruben Props, Nico Boon, Willem Waegeman · 2017

Absolute quantification of microbial taxon abundances Open

Ruben Props, Frederiek‐Maarten Kerckhof, Peter Rubbens, Jo De Vrieze, Emma Hernandez‐Sanabria , et al. · 2016

High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surve…

Learning in silico communities to perform flow cytometric identification of synthetic bacterial communities Open

Peter Rubbens, Ruben Props, Nico Boon, Willem Waegeman · 2016

Flow cytometry is able measure up to 50.000 cells in various dimensions in seconds of time. This large amount of data gives rise to the possibility of making predictions at the single-cell level, however, applied to bacterial populations a…

Clustering environmental flow cytometry data by searching density peaks Open

Peter Rubbens, Willem Waegeman, Ruben Props, Nico Boon · 2016

Microbial single cells can be characterized by their phenotypic properties using flow cytometry. Therefore flow cytometry can be used to analyze various aspects of environmental microbial communities. In recent years, researchers have focu…

Identifying synthetic microbial communities by learning in silico communities using flow cytometry Open

Peter Rubbens, Willem Waegeman, Ruben Props, Nico Boon · 2016

Single cells can be characterized in terms of their phenotypic properties using flow cytometry. However, up to our knowledge there has not yet been a thorough survey concerning the classification of bacterial species based on flow cytometr…

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