Jan Roelof van der Meer

The paper develops genome-scale metabolic models for a synthetic soil microbial community to understand metabolic interactions and community function.

The paper develops a mathematical framework to predict microbial community assembly using monoculture growth kinetics and inferred species interactions, revealing biphasic community development driven by competition and cross-feeding.

This study tracks microbial community assembly in soil bacteria, showing that spatial interactions and growth kinetics determine species success and community composition.

This study investigates the activation and transfer of ICEclc-like elements in Pseudomonas aeruginosa, showing that excision can be induced by stressors like copper and that excision and conjugation are uncoupled processes.

This study shows that habitat fragmentation increases bacterial community evenness and species coexistence by creating isolated microhabitats with varying taxa compositions.

The paper develops a modular genetic toolbox for gene regulation and multi-color imaging in streptococci by benchmarking fluorescent proteins and creating versatile cassettes for different species.

This study shows BisD, a ParB-like protein, coordinates gene activation and DNA segregation in ICEclc transfer competence development in Pseudomonas putida.

The paper identifies population-level control of two Mn oxidase genes in Pseudomonas putida, revealing how gene expression patterns regulate Mn biomineralization in microbial communities.

The paper investigates how microbiota origin affects transplant outcomes in soil, finding that habitat filtering, not origin, determines success.

The paper shows that fragmented microhabitats lead to more variable bacterial interactions, enabling alternative outcomes and supporting species diversity.

Bacttle is a microbiology board game designed to improve general microbiology knowledge in children and the public through gameplay and assessment.

Dimalis automates the analysis of bacterial cell growth from time-lapse imaging, providing standardized outputs for downstream processing.

This study develops and benchmarks coculture microcolony experiments to quantify interspecific interactions and growth kinetics in bacterial communities.

STrack is a tool for tracking bacterial cells in time-lapse microscopy images, showing high consistency across six bacterial strains.

The paper identifies a regulatory cascade controlling bistable transfer competence in ICEclc, showing it acts as an analog-to-digital converter through a feedback loop.

The paper integrates genome-scale metabolic modeling with transcriptomics and exometabolomics to predict bacterial metabolic responses and validate them experimentally in Pseudomonas veronii.

The paper identifies two distinct Acetobacteraceae clades in honey bees with diverging metabolic capabilities and ecological roles.

The paper computationally redesigns the Escherichia coli RbsB ribose-binding protein to recognize non-natural ligands 1,3-cyclohexanediol and cyclohexanol, achieving partial success with some mutants showing ligand-specific induction.