A5016375501- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Single-cell and spatial transcriptomics
- Biosensors and Analytical Detection
- Cell Image Analysis Techniques
- Innovative Microfluidic and Catalytic Techniques Innovation
- Genomics and Phylogenetic Studies
- Microfluidic and Bio-sensing Technologies
- Vibrio bacteria research studies
- Spectroscopy Techniques in Biomedical and Chemical Research
- Environmental DNA in Biodiversity Studies
- Pancreatic and Hepatic Oncology Research
- Bacterial Identification and Susceptibility Testing
- Wastewater Treatment and Nitrogen Removal
- Spectroscopy and Chemometric Analyses
- Gene Regulatory Network Analysis
- Molecular Communication and Nanonetworks
- Bacterial biofilms and quorum sensing
- Biomedical Text Mining and Ontologies
- Complex Network Analysis Techniques
- Coral and Marine Ecosystems Studies
- Neutrino Physics Research
- Marine Biology and Ecology Research
- Advanced Fluorescence Microscopy Techniques
- Water Treatment and Disinfection
Flanders Marine Institute
2019-2023
Ghent University
2015-2021
Ghent University Hospital
2014
Abstract Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks the increase amount data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine is needed marine ecology. Then we provide quick primer on techniques vocabulary. built database ∼1000 publications implement such analyse ecology For various types (images, optical spectra, acoustics, omics, geolocations, biogeochemical...
Isogenic bacterial populations are known to exhibit phenotypic heterogeneity at the single-cell level. Because of difficulties in assessing a single taxon mixed community, importance this deeper level organization remains relatively unknown for natural communities. In study, we have used membrane-based microcosms that allow probing while interacting with synthetic or community. Individual taxa were studied under axenic conditions, as members coculture physical separation, and culture....
In diagnostics of infectious diseases, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) can be applied for the identification pathogenic microorganisms. However, to achieve a trustworthy from MALDI-TOF MS data, significant amount biomass should considered. The bacterial load that potentially occurs in sample is therefore routinely amplified by culturing, which time-consuming procedure. this paper, we show culturing avoided conducting on individual...
Microorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied analysis of 16S rRNA gene sequences from DNA.
Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements up 50,000 per second. However, there has not yet been a thorough survey concerning the identification population which bacterial single belong based on data. This paper only aims assess quality data when measuring populations, but also suggests an alternative approach for analyzing synthetic microbial communities. We created so-called...
A major goal in microbial ecology is to understand how community structure influences ecosystem functioning. Various methods directly associate bacterial taxa functional groups the environment are being developed. In this study, we applied machine learning relate taxonomic data obtained from marker gene surveys identified by flow cytometry. This allowed us identify that associated with heterotrophic productivity freshwater lakes and indicated key contributors were highly system specific,...
Abstract Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing remains a challenge, as there is no standardized analysis framework. Several optical tools are available, such flow cytometry Raman spectroscopy, which describe properties of the individual cell. In this work, we compare spectroscopy study in bacterial populations. The growth stages three replicate Escherichia coli populations were characterized using both...
Introduction: Cyt-Geist: Current and Future Challenges in Cytometry 601 Chapter 01: Trends 01 Introduction WS18: Flow Drivers WS06: the Era of Human Cell Atlas 000 WS07: CYTO Lab Hacks: Inspiring Innovation Through Open Collaboration 605 WS15: The Status Microbiome 607 Conclusion 610 02: Shared Resource Laboratory (SRL) Best Practices 02 WS01: Balancing Science Service a 611 WS02: A Successful Imaging Facility: Guidelines for Management Publication 613 WS05: Identification Areas Where...
Multicolor approaches are challenging for microbial flow cytometry; as cytometers mainly developed biomedical applications, modern instruments contain more detectors than needed. Some of these additional fluorescence measure biological information due to spectral overlap, yet the extent which this is relevant identification bacterial populations ambiguous. In paper we characterize usefulness detectors. We propose a data-driven detector selection method select smallest subset that will...
Microbiome management research and applications rely on temporally resolved measurements of community composition. Current technologies to assess composition make use either cultivation or sequencing genomic material, which can become time-consuming and/or laborious in case high-throughput are required. Here, using data from a shrimp hatchery as an economically relevant study, we combined 16S rRNA gene amplicon flow cytometry develop computational workflow that allows the prediction taxon...
Abstract Recent years have seen an increased interest in employing data analysis techniques for the automated identification of cell populations field cytometry. These highly depend on use a distance metric, function that quantifies distances between single‐cell measurements. In most cases, researchers simply Euclidean metric. this article, we exploit availability labels to find optimal Mahalanobis metric derived from data. We show such results improved compared with Once determined, it can...
ABSTRACT Antiseptics are widely used in oral healthcare to prevent or treat diseases, such as gingivitis and periodontitis. However, the incidence of bacteria being tolerant standard antiseptics has sharply increased over last few years. This stresses urgency for surveillance against organisms, well discovery novel antimicrobials. Traditionally, susceptibility antimicrobials is assessed by broth micro-dilution disk diffusion assays, both which time-consuming, labor-intensive, provide limited...
Variations in the gut microbiome have been associated with changes health state such as Crohn’s disease. Most surveys characterize through analysis of 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report we analyzed a disease cohort has characterized by both technologies. Changes microbial community structure are reflected types data. We demonstrate cytometric fingerprints diagnostic tool order to classify samples according state. These results...
Abstract Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing remains a challenge, as there is no standardized analysis framework. Several optical tools are available, which often describe properties of the individual cell. In this work, we compare Raman spectroscopy flow cytometry study in bacterial populations. The growth phase E. coli populations was characterized using both technologies. Our findings show that...
Abstract Microbial flow cytometry allows to rapidly characterize microbial communities. Recent research has demonstrated a moderate strong connection between the cytometric diversity and taxonomic based on 16S rRNA gene amplicon sequencing data. This creates opportunity integrate both types of data study predict community in an automated efficient way. However, results number unique challenges that need be addressed. The our work are threefold: i) We expand current fingerprinting approaches...
Abstract Isogenic bacterial populations are known to exhibit phenotypic heterogeneity at the single cell level. Because of difficulties in assessing a taxon mixed community, importance this deeper level organisation remains relatively unknown for natural communities. In study, we have used membrane-based microcosms that allow probing while interacting with synthetic or community. Individual taxa were studied under axenic conditions, as members coculture physical separation, and culture....
Abstract 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 does not. However, which taxa specifically associated these groups, extension, productivity has remained elusive. Here, we addressed this knowledge gap using a machine learning-based variable selection approach that integrated FCM 16S rRNA gene sequencing data collected...