A5038303660- Microbial Metabolic Engineering and Bioproduction
- Gut microbiota and health
- Fungal and yeast genetics research
- Biofuel production and bioconversion
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Pharmacogenetics and Drug Metabolism
- Microbial Community Ecology and Physiology
Ollscoil na Gaillimhe – University of Galway
2023-2025
Wageningen University & Research
2019-2020
The human microbiome influences the efficacy and safety of a wide variety commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- molecule-resolved, scalable computational modeling. Here, we extend our previous resource genome-scale metabolic reconstructions gut microorganisms with greatly expanded version. AGORA2 (assembly organisms through reconstruction analysis, version 2) accounts for 7,302 strains, includes...
The human microbiome plays a crucial role in metabolism and thereby influences health disease. Constraint-based reconstruction analysis (COBRA) has proven an attractive framework to generate mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis within computational systems biology community. Unlike for human, no large-scale visualisation resource been available date. To address this gap, we created MicroMap, manually curated metabolic network visualisation, which...
Summary Computational modelling of microbiome metabolism has proved instrumental to catalyse our understanding diet-host-microbiome-disease interactions through the interrogation mechanistic, strain- and molecule-resolved metabolic models. We present APOLLO, a resource 247,092 human microbial genome-scale reconstructions spanning 19 phyla accounting for genomes from 34 countries, all age groups, five body sites. explored potential reconstructed strains developed machine learning classifier...
Abstract Motivation Computational approaches to the functional characterization of microbiome, such as Microbiome Modelling Toolbox, require precise information on microbial composition and relative abundances. However, challenges arise from homosynonyms—different names referring same taxon, which can hinder mapping process lead missed species when using metabolic reconstruction resources, AGORA APOLLO. Results We introduce integrated MARS pipeline, a user-friendly Python-based solution that...
Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for wide range compounds. Ethyl acetate is an industrial solvent that used in several applications, mainly as biodegradable organic with low toxicity. While ethyl produced by natural yeast species, the main mechanism production remained elusive until discovery Eat1 Wickerhamomyces anomalus. Unlike other alcohol acetyl transferases (AATs), located mitochondria, suggesting coding sequence...
Abstract Background: Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for wide range compounds. Ethyl acetate is an industrial solvent that used in several applications, mainly as biodegradable organic with low toxicity. While ethyl produced by natural yeast species, the main mechanism production remained elusive until discovery Eat1 Wickerhamomyces anomalus . Unlike other alcohol acetyl transferases (AATs), located mitochondria,...
Abstract Background Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for wide range compounds. Ethyl acetate is an industrial solvent that used in several applications, mainly as biodegradable organic with low toxicity. While ethyl produced by natural yeast species, the main mechanism production remained elusive until discovery Eat1 Wickerhamomyces anomalus . Unlike other alcohol acetyl transferases (AATs), located mitochondria,...