A5074725115- Microbial Metabolic Engineering and Bioproduction
- Gut microbiota and health
- Metabolomics and Mass Spectrometry Studies
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Diet and metabolism studies
- Biofuel production and bioconversion
- Metabolism and Genetic Disorders
- Genomics and Phylogenetic Studies
- Tryptophan and brain disorders
- Nutrition, Genetics, and Disease
- Pharmacogenetics and Drug Metabolism
- Parkinson's Disease Mechanisms and Treatments
- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- Enzyme Catalysis and Immobilization
- Drug Transport and Resistance Mechanisms
- Probiotics and Fermented Foods
- Mitochondrial Function and Pathology
- Folate and B Vitamins Research
- Computational Drug Discovery Methods
- Helicobacter pylori-related gastroenterology studies
- Bacterial Genetics and Biotechnology
- Process Optimization and Integration
- Biochemical and Molecular Research
Ollscoil na Gaillimhe – University of Galway
2019-2025
APC Microbiome Institute
2019-2025
University College Cork
2020-2024
National University of Ireland
2019-2023
University of Luxembourg
2013-2020
University of California, San Diego
2004-2017
University of Iceland
2009-2014
Brigham and Women's Hospital
2014
King's College London
2014
Harvard University
2014
Metabolism is a vital cellular process, and its malfunction major contributor to human disease. Metabolic networks are complex highly interconnected, thus systems-level computational approaches required elucidate understand metabolic genotype–phenotype relationships. We have manually reconstructed the global network based on Build 35 of genome annotation comprehensive evaluation >50 years legacy data (i.e., bibliomic data). Herein we describe reconstruction process demonstrate how...
The human gut microbiota supplies its host with essential nutrients, including B-vitamins. Using the PubSEED platform, we systematically assessed genomes of 256 common bacteria for presence biosynthesis pathways eight B-vitamins: biotin, cobalamin, folate, niacin, pantothenate, pyridoxine, riboflavin, and thiamin. On basis absence genome annotations, predicted that each vitamins was produced by 40-65% microbes. distribution synthesis diverse; some had all pathways, whereas others contained...
Metabolomics is the comprehensive study of metabolome, repertoire biochemicals (or small molecules) present in cells, tissues, and body fluids. The metabolism at global or "-omics" level a rapidly growing field that has potential to have profound impact upon medical practice. At center metabolomics, concept person's metabolic state provides close representation individual's overall health status. This reflects what been encoded by genome, modified diet, environmental factors, gut microbiome....
Flux variability analysis is often used to determine robustness of metabolic models in various simulation conditions. However, its use has been somehow limited by the long computation time compared other constraint-based modeling methods. We present an open source implementation flux called fastFVA. This efficient makes large-scale feasible and tractable allowing more complex biological questions regarding network flexibility be addressed. Networks involving thousands biochemical reactions...
A multitude of factors contribute to complex diseases and can be measured with 'omics' methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, www.vmh.life) database encapsulating current knowledge human metabolism within five interlinked resources 'Human metabolism', 'Gut microbiome', 'Disease', 'Nutrition', 'ReconMaps'. The VMH captures 5180 unique metabolites, 17 730 reactions, 3695 genes, 255 Mendelian diseases, 818...
Photosynthesis has recently gained considerable attention for its potential role in the development of renewable energy sources. Optimizing photosynthetic organisms biomass or biofuel production will therefore require a systems understanding processes. We reconstructed high-quality genome-scale metabolic network Synechocystis sp. PCC6803 that describes key processes mechanistic detail. performed an exhaustive silico analysis process under different light and inorganic carbon ( Ci )...
The human gut microbiome performs important functions in health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids their subsequent deconjugation transformation by the microbiome. To understand these system-level host-microbe interactions, a mechanistic, multi-scale computational systems biology approach that integrates different types omic data needed. Here, we use systematic workflow to computationally model acid metabolism...
Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach studying metabolism, whereas individual-based modeling commonly used to study complex dynamics interacting organisms. In this study, we combine both techniques into R package BacArena...
ABSTRACT The human gut microbiota plays a central role in well-being and disease. In this study, we present an integrated, iterative approach of computational modeling, vitro experiments, metabolomics, genomic analysis to accelerate the identification metabolic capabilities for poorly characterized (anaerobic) microorganisms. We demonstrate beneficial microbe Faecalibacterium prausnitzii strain A2-165. generated automated draft reconstruction, which curated against limited biochemical data....
The human gut microbiota consists of ten times more microorganisms than there are cells in our body, processes otherwise indigestible nutrients, and produces important energy precursors, essential amino acids, vitamins. In this study, we assembled validated a genome-scale metabolic reconstruction Bacteroides thetaiotaomicron (iAH991), prominent representative the microbiota, consisting 1488 reactions, 1152 metabolites, 991 genes. To create comprehensive model host-microbe interactions,...
Abstract The gut microbiome is a key player in the immunomodulatory and protumorigenic microenvironment during colorectal cancer (CRC), as different gut-derived bacteria can induce tumour growth. However, crosstalk between host relation to cell metabolism remains largely unexplored. Here we show that formate, metabolite produced by CRC-associated bacterium Fusobacterium nucleatum , promotes CRC development. We describe molecular signatures linking phenotypes with abundance. Cocultures of F....
Parkinson's disease (PD) is a systemic clinically defined by the degeneration of dopaminergic neurons in brain. While alterations gut microbiome composition have been reported PD, their functional consequences remain unclear. Herein, we addressed this question an analysis stool samples from Luxembourg Study (n = 147 typical PD cases, n 162 controls).All individuals underwent detailed clinical assessment, including neurological examinations and neuropsychological tests followed self-reporting...
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...
Increasing evidence suggests Alzheimer's disease (AD) pathophysiology is influenced by primary and secondary bile acids, the end product of cholesterol metabolism. We analyze 2,114 post-mortem brain transcriptomes identify genes in alternative acid synthesis pathway to be expressed brain. A targeted metabolomic analysis acids measured from samples 111 individuals supports these results. Our metabolic network that taurine transport, synthesis, metabolism differ AD cognitively normal...