A5041170743- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Enzyme Catalysis and Immobilization
- Gene Regulatory Network Analysis
- Microbial Community Ecology and Physiology
- Anaerobic Digestion and Biogas Production
- Viral Infectious Diseases and Gene Expression in Insects
- Fungal and yeast genetics research
- Gut microbiota and health
- Biomedical Text Mining and Ontologies
- Bacterial Genetics and Biotechnology
- Gene expression and cancer classification
- Protein Structure and Dynamics
- Microbial Metabolism and Applications
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- Antimicrobial Resistance in Staphylococcus
- Semantic Web and Ontologies
- Distributed and Parallel Computing Systems
- Amino Acid Enzymes and Metabolism
- Diet and metabolism studies
- Enzyme Structure and Function
- Tuberculosis Research and Epidemiology
Wageningen University & Research
2016-2025
Institut de Biologie systémique et synthétique
2013-2018
Bioengineering Center
2017
National Center for Genetic Engineering and Biotechnology
2017
John Wiley & Sons (United States)
2017
Hudson Institute
2017
Helmholtz Centre for Infection Research
2009-2012
Genopole (France)
2009-2011
Université d'Évry Val-d'Essonne
2009-2011
Centre National de la Recherche Scientifique
2008-2011
Titania (TiO₂)-based nanocomposites subjected to light excitation are remarkably effective in eliciting microbial death. However, the mechanism by which these materials induce death and effects that they have on microbes poorly understood. Here, we assess low dose radical-mediated TiO₂ photocatalytic action of such evaluate genome/proteome-wide expression profiles Pseudomonas aeruginosa PAO1 cells after two minutes intervention. The results indicate impact gene-wide flux distribution...
Significance Bacteria are constantly exposed to foreign elements, such as bacteriophages and plasmids. The CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR associated) adaptive immune systems provide heritable sequence-specific protection against these invaders. To develop immunity, bacteria add segments of nucleic acid their CRISPR memory. However, phage plasmid mutants can evade recognition by altering targeted sequence. responds evasion quickly generating...
ABSTRACT The composition and activity of the microbiota in human gastrointestinal tract are primarily shaped by nutrients derived from either food or host. Bacteria colonizing mucus layer have evolved to use mucin as a carbon energy source. One members mucosa-associated is Akkermansia muciniphila , which capable producing an extensive repertoire mucin-degrading enzymes. To further study substrate utilization abilities A. we constructed genome-scale metabolic model test amino acid auxotrophy,...
Summary Despite various efforts to develop tools detect and compare the catabolic potential activity for pollutant degradation in environmental samples, there is still a need an open‐source, curated reliable array method. We developed custom system including novel normalization strategy that can be applied any microarray design, allowing calculation of reliability signals make cross‐experimental comparisons. Array probes, which are fully available scientific community, were designed from...
The human pathogen Mycobacterium tuberculosis has the capacity to escape eradication by professional phagocytes. During infection, M. resists harsh environment of phagosomes and actively manipulates macrophages dendritic cells ensure prolonged intracellular survival. In contrast other pathogens, it remained difficult capture transcriptome mycobacteria during infection due an unfavorable host-to-pathogen ratio. We infected macrophage-like cell line THP-1 with attenuated surrogate bovis...
Abstract Gastrointestinal (GI) microbiota composition differs between breastfed and formula-fed infants. Today’s infant formulas are often fortified with prebiotics to better mimic properties of human milk respect its effect on GI function. We used Illumina HiSeq sequencing PCR-amplified 16S rRNA gene fragments investigate the faecal in 2–12 week old infants receiving either breastmilk, prebiotics, or mixed feeding. compared these results from fed traditional Netherlands 2002–2003, which...
Harnessing the power of microbial consortia is integral to a diverse range sectors, from healthcare biotechnology environmental remediation. To fully realize this potential, it critical understand mechanisms behind interactions that structure and determine their functions. Constraint-based reconstruction analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as state-of-the-art tool simulate behavior communities constituent genomes. In last decade, many...
Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) three compartments: two from stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) one submerged non-stratified mat biofilm. The communities colonising those the...
The zebrafish is a vertebrate model compatible with the paradigms of drug discovery. small size and transparency embryos make them amenable for automation necessary in high-throughput screenings. We have developed an automated platform vivo chemical screenings on that includes methods embryo dispensation, compound delivery, incubation, imaging analysis results. At present, two different assays to detect cardiotoxic compounds angiogenesis inhibitors can be automatically run platform, showing...
The microbiomes in the gastrointestinal tract (GIT) of individuals receiving antibiotics and those obese subjects undergo compositional shifts, metabolic effects linkages which are not clearly understood. Herein, we set to gain insight into these effects, particularly with regard carbohydrate metabolism, contribute unravel underlying mechanisms consequences for health conditions. We measured activity level GIT carbohydrate-active enzymes toward 23 distinct sugars adults patients (n = 2) 14-d...
Abstract Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering bioremediation. We analysed 432 sequenced strains by integrating results from large scale functional comparison using protein domains with data six metabolic models, nearly thousand transcriptome measurements four transposon mutagenesis experiments. Through heterogeneous integration we linked gene essentiality, persistence expression...
Summary The abundance of the human intestinal symbiont Akkermansia muciniphila has found to be inversely correlated with several diseases, including metabolic syndrome and obesity. A. is known use mucin as sole carbon nitrogen source. To study physiology potential for therapeutic applications this bacterium, we designed a defined minimal medium. composition medium was based on genome‐scale model mucin. Our results indicate that does not code GlmS, enzyme mediates conversion...
The nitrogen containing aromatic compound indole is known for its floral odor typical of jasmine blossoms. Due to characteristic scent, it frequently used in dairy products, tea drinks and fine fragrances. demand natural by the flavor fragrance industry high, yet, abundance essential oils isolated from plants such as narcissus low. Thus, there a strong sustainable method produce food-grade indole.Here, we established biotechnological production upon L-tryptophan supplementation bacterial...
Biostimulation is widely used to enhance reductive dechlorination of chlorinated ethenes in contaminated aquifers. However, the knowledge on corresponding biogeochemical responses limited. In this study, glycerol was injected an aquifer with cis-dichloroethene (cDCE), and geochemical microbial shifts were followed for 265 days. Consistent anoxic conditions sulfate reduction after biostimulation, MiSeq 16S rRNA gene sequencing revealed temporarily increased relative abundance Firmicutes,...
To unlock the full potential of genome data and to enhance interoperability reusability annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used process analyze existing annotations. automatically predicts, tracks stores structural functional associated dataset- element-wise provenance in Linked Data format, thereby enabling information mining retrieval Web...
The complex nature of the mechanisms behind cardiovascular diseases prevents detection latent early risk conditions. Network representations are ideally suited to investigate interconnections between individual components a biological system that underlies diseases. Here, we patterns correlations an array 29 metabolites identified and quantified in plasma 864 healthy blood donors use systems biology approach define metabolite probabilistic networks specific for low high risk. We adapted...
Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production commodity chemicals. To date, syngas focuses mainly on the use Clostridium species small organic molecules such as ethanol and acetate. The co-cultivation syngas-fermenting microorganisms with chain-elongating bacteria can expand range possible products, allowing, instance, medium-chain fatty acids (MCFA) alcohols from syngas. explore these possibilities, we report herein a genome-scale,...
Cutaneotrichosporon oleaginosus ATCC 20509 is a fast-growing oleaginous basidiomycete yeast that able to grow in wide range of low-cost carbon sources including crude glycerol, byproduct biodiesel production. When glycerol used as source, this can accumulate more than 50% lipids (w/w) with high concentrations mono-unsaturated fatty acids.To increase our understanding and provide knowledge base for further industrial use, FAIR re-annotated genome was build genome-scale, constraint-based...
Summary Genome‐scale, constraint‐based models (GEM) and their derivatives are commonly used to model gain insights into microbial metabolism. Often, however, accuracy predictive power limited enable only approximate designs. To improve usefulness for strain bioprocess design, we studied here capacity accurately predict metabolic changes in response operational conditions a bioreactor, as well intracellular, active reactions. We flux balance analysis (FBA) dynamic FBA (dFBA) growth dynamics...
Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, floral. In addition, it contributes to the flavor foods, applied fragrance industry. nature, indole synthesized either from tryptophan bacterial tryptophanases (TNAs) or indole-3-glycerol phosphate (IGP) plant lyases (IGLs). While widely accepted that synthase α-subunit (TSA) has intrinsically low IGL activity absence of β-subunit, this study, we show Corynebacterium glutamicum...