A5037356208- Bacterial Genetics and Biotechnology
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- RNA and protein synthesis mechanisms
- Drug Transport and Resistance Mechanisms
- Helicobacter pylori-related gastroenterology studies
- Biofuel production and bioconversion
- Anaerobic Digestion and Biogas Production
- Photosynthetic Processes and Mechanisms
- Diet and metabolism studies
- Bacteriophages and microbial interactions
- Biochemical and Molecular Research
- Metabolism and Genetic Disorders
- Pharmacogenetics and Drug Metabolism
- Amino Acid Enzymes and Metabolism
- Metabolomics and Mass Spectrometry Studies
- Porphyrin Metabolism and Disorders
- Enzyme Structure and Function
- Coenzyme Q10 studies and effects
- Vitamin K Research Studies
- Microbial metabolism and enzyme function
- Salmonella and Campylobacter epidemiology
Ollscoil na Gaillimhe – University of Galway
2019-2023
University of Luxembourg
2014-2019
Indian Institute of Science Education and Research, Bhopal
2019
International Centre for Genetic Engineering and Biotechnology
2019
Noida International University
2019
Institute for Information Transmission Problems
2005-2014
Sanford Burnham Prebys Medical Discovery Institute
2011-2014
Hope College
2011
Lomonosov Moscow State University
2005-2007
Russian Academy of Sciences
2005-2006
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...
Genome-scale prediction of gene regulation and reconstruction transcriptional regulatory networks in prokaryotes is one the critical tasks modern genomics. Bacteria from different taxonomic groups, whose lifestyles natural environments are substantially different, possess highly diverged networks. The comparative genomics approaches useful for silico bacterial regulons operated by both transcription factors (TFs) RNA elements (riboswitches).RegPrecise (http://regprecise.lbl.gov) a web...
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...
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...
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...
Bacteroides thetaiotaomicron, a predominant member of the human gut microbiota, is characterized by its ability to utilize wide variety polysaccharides using extensive saccharolytic machinery that controlled an expanded repertoire transcription factors (TFs). The availability genomic sequences for multiple species opens opportunity their comparative analysis enable characterization metabolic and regulatory networks. A genomics approach was applied reconstruction functional annotation...
Redox-sensing repressor Rex was previously implicated in the control of anaerobic respiration response to cellular NADH/NAD+ levels Gram-positive bacteria. We utilized comparative genomics approach infer candidate Rex-binding DNA motifs and assess regulon content 119 genomes from 11 taxonomic groups. Both DNA-binding NAD-sensing domains are broadly conserved orthologs identified phyla Firmicutes, Thermotogales, Actinobacteria, Chloroflexi, Deinococcus-Thermus, Proteobacteria. The showed...
Ethanolamine can be used as a source of carbon and nitrogen by phylogenetically diverse bacteria. Ethanolamine-ammonia lyase, the enzyme that breaks ethanolamine into acetaldehyde ammonia, is encoded gene tandem eutBC. Despite extensive studies utilization in Salmonella enterica serovar Typhimurium, much remains to learned about EutBC structure catalytic mechanism, evolutionary origin utilization, regulatory links between metabolism itself ethanolamine-ammonia lyase cofactor...
DNA-binding transcription factors (TFs) are essential components of transcriptional regulatory networks in Bacteria. LacI-family TFs (LacI-TFs) broadly distributed among certain lineages bacteria. The majority characterized LacI-TFs sense sugar effectors and regulate carbohydrate utilization genes. comparative genomics approaches enable silico identification TF-binding sites regulon reconstruction. To study function evolution LacI-TFs, we performed genomics-based reconstruction analysis...
Genome-scale prediction of gene regulation and reconstruction transcriptional regulatory networks in bacteria is one the critical tasks modern genomics. The Shewanella genus comprised metabolically versatile gamma-proteobacteria, whose lifestyles natural environments are substantially different from Escherichia coli other model bacterial species. comparative genomics approaches computational identification sites useful for silico bacteria. To explore conservation variations we analyzed...
The colonic mucus layer is a dynamic and complex structure formed by secreted transmembrane mucins, which are high-molecular-weight heavily glycosylated proteins. Colonic consists of loose outer dense epithelium-attached layer. inhabited various representatives the human gut microbiota (HGM). Glycans can be used HGM as source carbon energy when dietary fibers not sufficiently available. Both commensals pathogens utilize mucin glycans. Commensals mostly involved in cleavage glycans, while...
Biological nitrogen fixation plays a crucial role in the cycle. An ability to fix atmospheric nitrogen, reducing it ammonium, was described for multiple species of Bacteria and Archaea. Being complex sensitive process, requires complicated regulatory system, also, on level transcription. The transcriptional network extensively studied several representatives class Alphaproteobacteria. This includes activator NifA, working tandem with alternative sigma-factor RpoN as well oxygen-responsive...
Motivation: Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured motifs that are inverted direct repeats spaced motif pairs. However, these difficult to identify owing their high divergence. The structure included explicitly into the recognition algorithm improves efficiency for highly divergent well estimation of geometric parameters.
Rex, a transcriptional repressor that modulates its DNA-binding activity in response to NADH/NAD(+) ratio, has recently been found play role the solventogenic shift of Clostridium acetobutylicum. Here, we combined comparative genomic reconstruction Rex regulons 11 diverse clostridial species with detailed experimental characterization Rex-mediated regulation C. The reconstructed clostridia included genes involved fermentation, hydrogen production, tricarboxylic acid cycle, NAD biosynthesis,...
Ubiquinone and menaquinone are membrane lipid-soluble carriers of electrons that essential for cellular respiration. Eukaryotic cells can synthesize ubiquinone but not menaquinone, whereas prokaryotes both quinones. So far, most the human gut microbiome (HGM) studies have been based on metagenomic analysis. Here, we applied an analysis individual HGM genomes to identification biosynthetic pathways. In our opinion, shift from metagenomics is a pivotal milestone in investigation bacterial...
Because of the specific anatomical and physiological properties human intestine, a oxygen gradient builds up within this organ that influences intestinal microbiota. The microbiome has been intensively studied in recent years, certain respiratory substrates used by gut inhabiting microbes have shown to play crucial role health. Unfortunately, systematic analysis not previously performed determine capabilities (HGM). Here, we analyzed distribution aerobic anaerobic reductases 254 HGM genomes....
Hyperthermophilic bacteria from the Thermotogales lineage can produce hydrogen by fermenting a wide range of carbohydrates. Previous experimental studies identified large fraction genes committed to carbohydrate degradation and utilization in model bacterium Thermotoga maritima. Knowledge these enabled comprehensive reconstruction biochemical pathways comprising network. However, transcriptional factors (TFs) regulatory mechanisms driving this network remained largely unknown. Here, we used...
Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic systems controlled by multiple transcription regulators. Thus, in E. global control respiration is mediated four factors, Fnr, ArcA, NarL NarP. However, other Gamma-proteobacteria the composition regulators may be different.In this study we applied comparative genomic approach to analysis three regulatory systems, ArcA These were studied available genomes...
Transcriptional regulatory networks are fine-tuned systems that help microorganisms respond to changes in the environment and cell physiological state. We applied comparative genomics approach implemented RegPredict Web server combined with SEED subsystem analysis available information on known interactions for network reconstruction human pathogen Staphylococcus aureus six related species from family Staphylococcaceae. The resulting reference set of 46 transcription factor regulons contains...
ABSTRACT The hexuronate metabolism in Escherichia coli is regulated by two related transcription factors from the FadR subfamily of GntR family, UxuR and ExuR. controls d -glucuronate metabolism, while ExuR represses genes involved all hexuronates. We use a comparative genomics approach to reconstruct metabolic pathways transcriptional regulons gammaproteobacteria. demonstrate differences binding motifs ExuR, identify new candidate members UxuR/ExuR regulons, describe links between adjacent...
Bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. In various bacteria, transcription of these genes is controlled GntR family factors (TFs) MatR/MdcY and/or LysR factor MdcR. Propionate metabolized methylcitrate pathway, comprising enzymes prp acn PrpR, Fis sigma 54-dependent factor, known to be a transcriptional activator Here, we report detailed comparative genomic analysis propionate metabolism its regulation in proteobacteria. We characterize loci gene...
Abstract Background Genome scale annotation of regulatory interactions and reconstruction networks are the crucial problems in bacterial genomics. The Lactobacillales order bacteria collates various microorganisms having a large economic impact, including both human animal pathogens strains used food industry. Nonetheless, no systematic genome-wide analysis transcriptional regulation has been previously made for this taxonomic group. Results A comparative genomics approach was 30 selected...
Bacterial microcompartments are self-assembling subcellular structures surrounded by a semipermeable protein shell and found only in bacteria, but not archaea or eukaryotes. The general functions of the bacterial to concentrate enzymes, metabolites, cofactors for multistep pathways; maintain cofactor ratio; protect cell from toxic metabolic intermediates; encapsulated pathway unwanted side reactions. were suggested play significant role organisms human gut microbiome, especially various...
Abstract The human microbiome influences the efficacy and safety of a wide variety commonly prescribed drugs, yet comprehensive systems-level approaches to interrogate drug-microbiome interactions are lacking. Here, we present computational resource microbial genome-scale reconstructions, deemed AGORA2, which accounts for 7,206 strains, includes drug degradation biotransformation, was extensively curated based on comparative genomics literature searches. AGORA2 serves as knowledge base...