A5020329649- Microbial Metabolic Engineering and Bioproduction
- Gut microbiota and health
- Biofuel production and bioconversion
- Fungal and yeast genetics research
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Fermentation and Sensory Analysis
- Enzyme Catalysis and Immobilization
- Clostridium difficile and Clostridium perfringens research
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Biochemical and biochemical processes
- Genomics and Phylogenetic Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Plant biochemistry and biosynthesis
- Evolution and Genetic Dynamics
- CRISPR and Genetic Engineering
- Tryptophan and brain disorders
- RNA and protein synthesis mechanisms
- Microbial Natural Products and Biosynthesis
- RNA Research and Splicing
- Evolutionary Game Theory and Cooperation
- Epigenetics and DNA Methylation
- Computational Drug Discovery Methods
University of Cambridge
2020-2025
Medical Research Council
2020-2025
MRC Toxicology Unit
2020-2025
European Molecular Biology Laboratory
2015-2024
Symbiosis International University
2024
European Molecular Biology Laboratory
2015-2024
Heinrich Heine University Düsseldorf
2024
Forschungszentrum Jülich
2024
University of Sharjah
2023
Himgiri Zee University
2022
Microbial communities populate most environments on earth and play a critical role in ecology human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as metabolite exchanges, have also been implicated community assembly. The prevalence of metabolic interactions microbial communities, however, has remained unknown. Here, we systematically survey, using genome-scale modeling approach, extent...
Cellular response to genetic and environmental perturbations is often reflected and/or mediated through changes in the metabolism, because latter plays a key role providing Gibbs free energy precursors for biosynthesis. Such metabolic are exerted transcriptional induced by complex regulatory mechanisms coordinating activity of different pathways. It difficult map such global responses using traditional methods, many genes network have relatively small at their transcription level. We...
Genome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding microbial communities. Yet, the application genome-scale models, especially to communities, is lagging behind availability sequenced genomes. This largely due time-consuming steps manual curation required obtain good quality models. Here, we present an automated tool, CarveMe, reconstruction species community level We...
Abstract Background Through genetic engineering it is possible to introduce targeted changes and hereby engineer the metabolism of microbial cells with objective obtain desirable phenotypes. However, owing complexity metabolic networks, both in terms structure regulation, often difficult predict effects modifications on resulting phenotype. Recently genome-scale models have been compiled for several different microorganisms where structural stoichiometric inherently accounted for. New...
Over the last few years a number of methods have been proposed for phenotype simulation microorganisms under different environmental and genetic conditions. These used as basis to support discovery successful modifications microbial metabolism address industrial goals. However, use these has restricted bioinformaticians or other expert researchers. The main aim this work is, therefore, provide user-friendly computational tool Metabolic Engineering applications. OptFlux is an open-source...
Many microorganisms live in communities and depend on metabolites secreted by fellow community members for survival. Yet our knowledge of interspecies metabolic dependencies is limited to few with small number exchanged metabolites, even less known about cellular regulation facilitating exchange. Here we show how yeast enables growth lactic acid bacteria through endogenous, multi-component, cross-feeding a readily established community. In nitrogen-rich environments, Saccharomyces cerevisiae...
Abstract Background Vanillin is one of the most widely used flavouring agents, originally obtained from cured seed pods vanilla orchid Vanilla planifolia . Currently vanillin mostly produced via chemical synthesis. A de novo synthetic pathway for heterologous production glucose has recently been implemented in baker's yeast, Saccharamyces cerevisiae In this study we aimed at engineering cell factory towards improved productivity and thereby developing an attractive alternative to Results...
Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition end-products, but also their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible food fermentations. Their niche depends on own properties as well those the other species. Here, we apply computational approach, which uses only genomic and metagenomic information functional annotation genes, to find that...
Abstract Microbial communities are composed of cells varying metabolic capacity, and regularly include auxotrophs that lack essential pathways. Through analysis for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial obtained as part the Earth Microbiome Project (EMP), study auxotrophic–prototrophic interactions self-establishing metabolically cooperating yeast (SeMeCos), we reveal a imprinted mechanism links presence to an increase gains...
Differentiating stem cells must coordinate their metabolism and fate trajectories. Here, we report that the catalytic activity of glycolytic enzyme Enolase 1 (ENO1) is directly regulated by RNAs leading to metabolic rewiring in mouse embryonic (mESCs). We identify RNA ligands specifically inhibit ENO1's enzymatic vitro diminish glycolysis cultured human mESCs. Pharmacological inhibition or RNAi-mediated depletion protein deacetylase SIRT2 increases acetylation enhances its binding....
A role for vitamin D in immune modulation and cancer has been suggested. In this work, we report that mice with increased availability of display greater immune-dependent resistance to transplantable cancers augmented responses checkpoint blockade immunotherapies. Similarly, humans, D-induced genes correlate improved inhibitor treatment as well immunity overall survival. mice, is attributable the activity on intestinal epithelial cells, which alters microbiome composition favor
Abstract To cope with oxidative stress, the metabolic network of plant cells must be reconfigured either to bypass damaged enzymes or support adaptive responses. characterize dynamics change during heterotrophic Arabidopsis (Arabidopsis thaliana) were treated menadione and changes in metabolite abundance 13C-labeling kinetics quantified a time series samples taken over 6 h period. Oxidative stress had profound effect on central pathways extensive inhibition radiating from tricarboxylic acid...